If there is more than one element in a glyph, then by default you can only edit the contours of the current element.

To edit across elements, turn on Edit > Edit Across Elements. Once this option is turned on, then you can perform contour editing operations (using tools like Contour, Eraser, Knife) across multiple elements in the same glyph.

In the Glyph Window or Sketchboard, by default, you can only edit contours on the currently selected layer or master.

To edit across layers, turn on Edit > Edit Across Layers. Once this option is turned on, you can edit contours across different layers and masters within the same glyph (the Edit Across Elements option must be active as well) or even across glyphs (if Edit Across Glyphs is also active).